Software

Citable software

1. GNOM: An optimized steady-state model of the modern global marine neodymium cycle Benoît Pasquier, Sophia K. V. Hines, Hengdi Liang, Yingzhe Wu, Steven L. Goldstein, Seth G. John 2021 doi: 10.5281/zenodo.5651295
2. F1Method.jl: A julia package to autodifferentiate through a steady-state solver Benoît Pasquier 2019 doi: 10.5281/zenodo.2667835
   • Abstract

   This package implements the F-1 algorithm described in Pasquier and Primeau (in preparation). It allows for efficient quasi-auto-differentiation of an objective function defined implicitly by the solution of a steady-state problem.

3. AIBECS.jl: A tool for exploring global marine biogeochemical cycles Benoît Pasquier, François W. Primeau, Seth G. John 2019 doi: 10.5281/zenodo.2864051
4. WorldOceanAtlasTools.jl: Download and process World Ocean Data in Julia Benoît Pasquier 2019 doi: 10.5281/zenodo.2677666
5. HyperDualNumbers.jl Rob J. Goedman, Nicola, Benoît Pasquier, Timothy Holy, Alexander Ronald Altman, Christopher Rackauckas, Tony Kelman, Viral B. Shah, Jishnu Bhattacharya 2018 doi: 10.5281/zenodo.1660762
   • Abstract

   Julia implementation of HyperDualNumbers.

6. HyperDualMatrixTools.jl Benoît Pasquier 2018 doi: 10.5281/zenodo.1670841
   • Abstract

   A little Julia module to allow factorization and backslash to work with hyperdual-valued arrays and sparse arrays.

7. DualMatrixTools.jl Benoît Pasquier 2018 doi: 10.5281/zenodo.1493571
   • Abstract

   A little Julia module to allow factorization and backslash to work with dual-valued arrays and sparse arrays.

Software contributions

1. UnitfulRecipes.jl Benoît Pasquier, David E Gustavsson, Jan Weidner, Jeff Fessler, Daniel Boland, Bart Janssens, Dilum Aluthge, Rafael Schouten, Claire Foster Plotting data with units seamlessly in Julia.
2. OceanographyCruises.jl Benoît Pasquier An interface for dealing with oceanographic cruises data
3. OceanGrids.jl Benoît Pasquier Standard format of grids for AIBECS
4. OceanBasins.jl Benoît Pasquier Programmatically determine which ocean basin a (lat,lon) coordinate is in
5. Inpaintings.jl Benoît Pasquier Julia version of MATLAB's inpaint_nans
6. GEOTRACES.jl Benoît Pasquier, Anshul Singhvi A package for reading and using GEOTRACES data in Julia
7. Earth2014.jl Benoît Pasquier, Yakir Luc Gagnon Download topographic data for the globe
8. BlockDiagonalFactors.jl Benoît Pasquier Efficiently solve linear block-diagonal systems with repeated blocks

Minor software contributions

1. offsetaxis-pkg Kelly Kearney, Benoît Pasquier OFFSETAXIS Add an x- or y-axis offset from the plotted axis area (MATLAB).
2. latexdiff Frederik Tilmann, Yarden Peleg, Benoît Pasquier, Joachim Protze, Tom de Geus, and many contributors Compares two latex files and marks up significant differences between them.
3. cmap Timothy Sipkens, Benoît Pasquier Perceptually uniform colormaps for MATLAB, compiled from multiple sources.
4. YAXArrays.jl Fabian Gans, Felix Cremer, Lazaro Alonso, Guido Kraemer, Pavel V. Dimens, Daniel Loos, Daniel E. Pabon-Moreno, Martin Reinhardt, and many contributors Yet Another XArray-like Julia package.
5. UnitfulMoles.jl Rafael Schouten, Benoît Pasquier Utilities for working with Mole units for the Julia language.
6. Unitful.jl Andrew Keller, and many contributors Julia package for physical units.
7. SciMLBase.jl Christopher Rackauckas, Aayush Sabharwal, Arno Strouwen, Qingyu Qu, Valentin Kaisermayer, Avik Pal, Vaibhav Kumar Dixit, Alex Jones, Oscar Smith, Lorenzo Van Munoz, Yingbo Ma, Sharan Yalburgi, Anshul Singhvi, and many contributors The Base interface of the SciML ecosystem.
8. RecipesBase.jl Tom Breloff, Chris Rackauckas, Daniel Schwabeneder, Simon Christ, and many contributors Base package for defining transformation recipes on user types for Plots.jl.
9. Plots.jl Tom Breloff1, and many contributors Powerful convenience for Julia visualisations and data analysis.
10. Makie.jl Simon Danisch, Julius Krumbiegel, and many contributors Interactive data visualisations and plotting in Julia.
11. InverseDistanceWeighting.jl Júlio Hoffimann, Benoît Pasquier Inverse distance estimation solver for the GeoStats.jl framework.
12. Interpolations.jl Tim Holy, Mark Kittisopikul, Alex Wadell, Tomas Aschan, Miles Lucas, Spencer Lyon, and many contributors Fast, continuous interpolation of discrete datasets in Julia.
13. GeoStats.jl Júlio Hoffimann, and many contributors Comprehensive framework for geostatistics (or spatial statistics).
14. Distributions.jl Dahua Lin, David Widmann, Simon Byrne, John Myles White, Andreas Noack, Mathieu Besançon, Douglas Bates, John Pearson, John Zito, Alex Arslan, Moritz Schauer, Kevin Squire, David Anthoff, Theodore Papamarkou, Jan Drugowitsch, Benjamin Deonovic, Avik Sengupta, Seth Axen, Brian J Smith, Glenn Moynihan, Giuseppe Ragusa, Martin O'Leary, Michael, Mohamed Tarek, Viral B. Shah, Christoph Dann, Mike J Innes, Tamas K. Papp, and many contributors A Julia package for probability distributions and associated functions.
15. DiffEqOperators.jl Christopher Rackauckas, Alex Jones, ajozefiak, Shivin Srivastava, Valentin Sulzer, Mohammed Jeeshan Sheikh, Emmanuel Lujan, Yingbo Ma, Xingjian Guo, William Chen, and many contributors Linear operators for discretizations of differential equations and scientific machine learning (SciML).
16. DiffEqBase.jl Christopher Rackauckas, Kanav Gupta, Yingbo Ma, Avik Pal, Jared Lumpe, David Widmann, Lilith Orion Hafner, Takafumi Arakaki, Daniel González Arribas, Oscar Smith, and many contributors DiffEqBase.jl is a component package in the DiffEq ecosystem.
17. CMAP.jl Mohammad Ashkezari, Benoît Pasquier Simons CMAP Julia client.